ATAC-Seq Protocol for MCF7 and LOXIMVI

ATAC-seq was performed as described [39 (link)], with the major exception of the use of a MuA transposase (Thermo) rather than the TN5 transposase. Briefly, MCF7 or LOXIMVI cells were trypsinized and 50 K cells, spun down, washed once with PBS, and lysed with a hypotonic buffer containing 0.1% NP-40, and spun down to generate a crude nuclei pellet. This pellet was transposed in a 30 μl volume using MuA (0.7 μl), MuA buffer (10 μl), and H2O (19 μl) for 5 min at 30C. The sample was treated with 3 μl stop solution, and incubated at 30C for a further minute. The sample was then collected and purified by addition of 45 μl of SPRI beads (Aline Biosciences). The purified sample was PCR amplified in two steps to add barcoded adaptors suitable for Illumina sequencing. Samples were sequenced with single end 75 bp reads on an Illumina NextSeq. Reads (> 30 M) were trimmed to remove adaptors with cutadapt [38 ], aligned to the genome with Bowtie, and analyzed with Matlab. Genomic DNA (50 ng) from MCF7 and LOXIMVI was transposed, amplified and sequenced in parallel to estimate background.